There are many routines for truing your table top. The easiest is to use the Table Surfacer Virtual Tool [TU] that generates a part file that's customized to your tool and surfacing bit. After it is finished cutting you will probably have to sand your top to remove any ridges left by the bit; just take off the high points. Re-check your top and if necessary drop the z-axis a little and rerun the truing routine.
To accurately cut your parts, especially the scarfs, it is really important to have a way to hold the plywood tightly to the table. Several ShopBot owners have devised methods to hold their plywood down using the vacuum of a ShopVac or dust collector. If you need ideas, there are pictures of my vacuum holddown setup on my web site at www.seasidesmallcraft.com .
